Pokemon: Weapon of Arceus
by Zoobeeny
Summary: When the pokemon world is corrupted by the power of the legendaries, the world is thrown into a massive war. Enter Lewis, a young boy with an uncanny ability to understand pokemon, have perfect memory recall, and strangely, the ability to use pokemon attacks. Join this young boy as he faces the real world after the Golden Age of Pokemon ended.
1. Chapter 1

**Hello readers. This is my second fanfic! Yay! No, I'm not done with the first, but with the release of Pokemon Go and such, well, I couldn't resist. So anyways, this chapter is 2200 words (don't expect the others to be as long) and this is the main reason my other fanfic hasn't gotten much progress, plus, you know, vacation and stuff. Well, I hope you enjoy this chapter, and maybe, if I ever finish, the story.**

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"And then, there was the really big explosion! Luckily, the main character managed to use the secret pool under the floor to escape!" exclaimed a young 12 year old boy. He was around five feet tall (about 1.6 - 1.7 meters tall) with a mess of brown hair, bright, green eyes, and an animated expression on his face. He sat across from a large cage containing a pokemon.

"What happened next?" asked a small green turtle pokemon with a twig on its head.

"I'll tell you next time, Clark," said the boy, smiling trollishly.

"You! TELL MEEEEEEEEE," cried the Turtwig, an expression of hopelessness on his face. "Pleeeease, Lewis? Pleeeeeeeease?"

"Nope." Lewis, the boy, turned his head and sniffed. "And I'm not changing my mind, no matter what you do."

"Lewis, are you bullying Clark again?" asked another pokemon, this one, a Kirlia who sat in the cage adjacent to Clark's.

"Layla, Lewis is bullying me again!" whined Clark, cutting off anything Lewis wanted to say.

"That's not true!" retorted Lewis. "I'm just keeping you in suspense!"

"That's called bullying," said Clark, pouting. The three of them began arguing about what bullying really was.

"Would all you children please silence yourselves? I am attempting to acquire some sleep." An old Lucario lay on his back in yet another cage. He had one eye opened and stared at the three kids who were arguing amongst themselves in increasingly loud voices.

"Oh, sorry for waking you up, Mercurius, I didn't know you were asleep," apologized Lewis. Layla and Clark nodded twice in agreement with Lewis.

"As a general of thumb, when one is silent, they normally do not want to be disturbed by loud children such as yourself." The Lucario sat up and sighed heavily. "However, I have already been awoken, as such, attempting to return to my slumber would be in vain."

"Heh, sorry…" Lewis smiled cheesily and scratched the back of his head.

"Lewis! Where are you!?" yelled someone from outside the room that Lewis currently resided within. "It's time for dinner!"

"Coming dad!" shouted Lewis. "Sorry guys, gotta go, I'll see you all tomorrow!" Quickly, Lewis ran out of the room, closing the door with a soft click. Technically speaking, Lewis wasn't allowed to be in that room. The scientists and other people had said that it was filled with flesh-eating monsters, but Lewis thought they were just joking. Clark did bite Lewis sometimes, anyways, so they weren't lying necessarily.

"Lewis, there you are." A tall, old man wearing a white lab coat strode up to the boy with a smile. "What are you doing here?"

"Nooothing…" said Lewis, trying to hide his own smile.

"Lewis, were you in there again?" asked Lewis' father. "You know you're not supposed to be in there, you might get hurt."

"But dad, they're really friendly and everything!" argued Lewis.

"Lewis, you remember what happened to Daniel, with the Alakazam, don't you?" asked Lewis' father. "I don't want you to end up like him."

"That's only because you were hurting Arkah!" countered Lewis. "If you weren't doing whatever it is you did to him, I bet Daniel wouldn't have been as badly injured as you said he was- MMhm!"

"Shh, Lewis!" Lewis' father clapped his hand over his son's mouth. "Do you remember something else we talked about? You're not to speak about how you can talk to the pokemon, do you understand? Bad things will happen if someone overhears you!"

"Mmph." Lewis' father took his hand off of Lewis' mouth and wiped it on his lab coat.

"Now let's go, and I don't want to hear you say anything about that Alakazam, do you understand?"

"Yeah yeah." Lewis sighed and followed his father to the dining hall. The smell of food was strong as they took their seat in the large hall. The food was relatively simple, comprised of a meat, some bread, and a soupy thing or vegetable. Today's menu was mystery meat with dry bread and something resembling soup. Lewis knew that the world was having it tough, how tough, he didn't know, so he was grateful for any food he got. Ordinarily, Lewis would've chomped through his food like a ravenous beast, but this time, his mind was occupied with thoughts about Arkah, the Alakazam.

Arkah had been an extremely vocal pokemon, at least to Lewis anyways. Arkah was almost always complaining about how the humans treated pokemon or how much smarter he was than them and how he should be the one commanding the humans. But then, one day, the scientists took him to a super secret area behind a large metal door that could only be opened by the scientist's fingerprints. When Arkah came back his eyes were bloodshot and he was completely silent.

"Lewis? Are you alright?" asked Lewis' father. "You don't seem like yourself today."

"Nah dad, I was just thinking really hard about something," said Lewis, stretching his back. Then, out of the corner of his eye, he saw an odd sight. Three scientists wearing hazmat suits, but that wasn't the worst thing. They were pushing a metal cage with a small, white, sleeping pokemon with light green hair.

"Layla…?" murmured Lewis, slowly standing up.

"Lewis? What's up?" Lewis didn't hear his father and began walking towards the direction that his friend had gone.

"Sorry, dad, I'll be back soon," he said without turning around. Lewis began to run after the scientists. They already had a huge head start, but they weren't running like Lewis was. It only took a minute for Lewis to catch up.

"What are you guys doing!?" he shouted at them, trying to get their attention. They didn't appear to hear him, and if they did, they ignored him. The scientists kept wheeling the cage down and approached the metal door.

"Hello!?" yelled Lewis, not even fifty feet from the scientists (that's about 14 meters, give or take). He would've made it, save for one reason. Instead of a normal door, the metal door simply faded away, allowing the scientists to get in without stopping. Just as Lewis made it to the scientists, they passed through the doorway and the metal door reappeared. Lewis slammed into the door and bounced off.

"Hey! Bring her back!" he yelled to no extent. Lewis banged on the door several times, but no response was given. Lewis leaned his back against the metal door and slid down. A quick glance at a nearby clock told Lewis that it was 7:11. He sighed, closed his eyes, and waited.

And time passed...

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"Hey, kid. Kid. Wake up, kid." Lewis was awakened by a soft nudge from someone's foot. He looked up into the face of one of the scientists, an old man with no hair left and one eye missing.

"Whaaa…?" asked Lewis sleepily. "What happened?"

"What are you doing here kid, you know this place is supposed to be off-limits," said the scientist. "And you've been here for quite some time now-" Lewis bolted to his feet and looked at a digital clocking hanging on the wall. It read 1:24.

"I've been here for six hours!?" he exclaimed in shock. "But how? They didn't even come this way!" A sudden thought struck Lewis and he quickly took out a map of the laboratory that he had drawn from memory. The areas that were restricted had dotted lines representing where Lewis guessed the walls to be, and judging from the overall size of the laboratory, Lewis' map showed that there could potentially be a second entrance to the secret laboratory room.

"Hey kid, is that a ma-" started the scientist.

"Sorry, gotta run!" called out Lewis, beginning to run again. Lewis ran as fast as he could back to the room with his friends all the while thinking, please don't be hurt, please don't be hurt, please don't be hurt. He repeated that in his head like a mantra, hoping against hope that she wasn't like Arkah. Turning a corner, Lewis ran straight at the door to the room of his friends and burst inside.

"Layla!" He yelled as soon as he stopped, noticing Mercurius with his paw sticking through the bars of his cage and into Layla's. A soft blue glow shone from the tip of his paw.

"Silence!" barked Mercurius. "She is trying to rest…" Lewis clamped his mouth shut and walked over to Layla's cage. However, Lewis didn't see Layla inside, or at the very least, he didn't think it was Layla. A Gardevoir lay inside the cage, sleeping with its eyes forcefully shut.

"Layla…?" Lewis dropped to his knees and poked the unmoving body of the Gardevoir.

"Did I not just say she is resting?!" said Mercurius nearly shouting. "And do not irritate her, she is in a critical stage as of now."

"W-What happened?" asked Lewis, his hands trembling.

"It was a forced evolution…" muttered Mercurius. "An unnatural form of the evolution stones… the humans have pushed it too far, they have actually achieved the impossible, and broken the DNA of Pokemon…"

"Uuh, what?" asked Clark, who was busy trying to reach Layla through the bars of his cage.

"Exactly as it sounds. By altering certain genes in Layla's body, and possibly introducing foreign materials into her body, they have induced an evolution." The blue light from Mercurius faded away and he dropped his arm. Layla slowly opened her eyes and sat up, breathing heavily.

"W-Where am I?" she asked, rubbing her head. "What happened?"

"Layla! You're okay!" exclaimed Lewis happily. "Do you feel alright?"

"Umm… I guess so…?" Layla leaned her back on the bars of her cage blinked several times before shaking her head to clear any dizziness. "So… what happened again?"

"You underwent an evolution it would seem," said Mercurius, clearly not telling her everything. "Are you feeling any pain anywhere?"

"An evolution!?" Layla immediately began to examine herself all over.

"Why're you so upset? I would love to evolve!" said Clark, frowning at Layla, who was in a state of pure panic.

"Clark, do try to understand that Layla is in a stage of shock," said Mercurius. "Please do not try to aggravate her further."

"But seriously! I don't get what's the big fuss about-" Clark was cut short by a blast of blue light from Mercurius.

"Guys, come on! That's beyond the point," said Lewis more than annoyed with his friends. He turned back to Layla. "You're not in any pain, right?"

"No, I'm just really tired- What's Arkah doing?" she suddenly asked, weakly pointing at the Alakazam's cage in the corner. Arkah gripped his knees to his chest, curled up in a ball, shaking back and forth, muttering all the while.

"They've done it. It's all their fault. They've done it. It's all their fault." Arkah repeated it over and over again. His eyes were wide and wild, roaming all over the place. The ground began to tremble and an awful wrenching noise could be heard. It was akin to fingernails wrenching across a blackboard, slowly and steadily progressing to be even more and more than it was previously.

"Arkah! Stop this infernal noise!" shouted Mercurius over the ear-grating noise. Seconds later, it stopped without warning.

"Ooookay, someone explain that to me," said Clark, narrowing his eyes. "What the heck was that?" There was no time for an explanation, for at the very moment Clark finished his question, an explosion of pure psychic power blasted outwards from Arkah.

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 **So, you made it to the bottom. Did you like it? Was it good? Was it bad? Was it weird? Leave a review, if you really want to, it doesn't really mean anything. Whatever, if you liked it, stay tuned, it might come, it might not. Whatever, I'll see you whenever I post another chpater. Ciao!**

 **Edit: This story was slightly altered due to some complaints about a joke made. The user said that they were inappropriate for this story, rated as T, and unless I moved it to M, would it be acceptable. I didn't really want to move it to _that_ level, so I had to remove the joke. Besides that, I removed the introduction paragraphs as that was irritating some people. Not gonna name anyone, but you could always just check the reviews. Beyond that, not much else to say. I'll just BS the rest of the story as I go. Ciao.**


	2. Chapter 2

**So here's Chapter 2. Ummm, not much to say, but my original course for the story has completely shifted, so, that irks me a bit, but whatevs. Anyways, this chapter is a whopping 2300 words by itself. Yeah. Anyways, hope you enjoy the chapter!**

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Lewis breathed in very slowly, turning ever so slightly to survey the floating objects that surrounded him. Fragments of metal were suspended in the air, seemingly levitating. Fighting back against the urge to touch one of the pieces of metal, Lewis tried to see if he could find anyone else among the maze of metal.

"Lewis! Do not move!" came Mercurius' voice from behind Lewis. "There is an extremely large metal shard very near to your back, should you so much as turn, it will likely pierce you."

"O-Oh… okay then…" said Lewis, gulping. "A-Are Layla and Clark okay?"

"Yes, they are fine," said Mercurius. "It would seem that the wave we felt was purely mental, while the energy the metal shards are under, would be more on the physical side."

"Th-That m-makes sense, I guess…" Lewis turned back around and looked straight in front of himself. There, floating in midair, was Arkah, turned a black color, save for his eyes, now purely white.

" _ **Finally… My time has finally come…**_ " said Arkah in a deep voice, unlike his original voice. " _ **It is time to rain my vengeance down upon those that call themselves our masters…**_ " Another wave of psychic energy vibrated outwards from Arkah's area, and all the metal shards were pulled towards him.

"Arkah?" Lewis couldn't believe what he was seeing. The metal shards were melting mid-flight towards Arkah and reforming themselves into a layer of armor over Arkah's body. The dark Alakazam landed on the ground and stepped towards the three other cages in the room.

" _ **Be free, my friends, and let us taste the sweetness of victory!**_ " said Arkah as all three cages shattered into pieces instantaneously.

"Arkah, what have you done…?" asked Mercurius, getting to his feet, something he hadn't done for many years. "This is not to say I am not grateful to you for releasing us, but…"

" _ **The time for answers is not now, my old friend, now is the time for us to take back our freedom from those that enslave us!**_ " Arkah proclaimed, pushing past Mercurius. " _ **Rise, allies, and join me!**_ " Raising his hand upwards, Arkah began to chant in a mysterious and unknown language. The ground trembled again and a thick, black slime, the same color as Arkah, started to ooze out of the ground at an alarming pace.

"Lewis, get over here, now," ordered Mercurius, watching the ground for the black slime. Lewis hurried over and picked up an unconscious Clark along the way.

"I can't get Layla, she's too heavy!" said Lewis, trying to drag Layla unsuccessfully.

"You stay right there, I'll grab her," said Mercurius, walking back to grab Layla. The slime was starting to fill up the room, but it didn't seem to stop, in fact, to Lewis, the slime's acceleration seemed to actually increase, filling the room at a faster speed than it had before.

"Huh? Lewis? Where are we?" asked Clark, waking up suddenly. "Why does it smell so… oh my…" The black slime was now halfway up Lewis' calves and Lewis could feel the strange greasiness and unnatural feeling that the slime generated.

"I got her!" said Mercurius, wading back with an unconscious Layla in his arms. The slime continued to flow in from somewhere, filling the room even more.

"Arkah! Please stop!" yelled Lewis, almost begging. "Arkah!" But the Alakazam was to deep into his chanting that nothing anyone said could break his concentration.

"I don't want to die like this!" said Clark, clambering onto Lewis' head. The slime was up to Lewis' waist when, miraculously, it stopped.

" _ **That should be enough for now…**_ " said Arkah, releasing whatever sorcery, for it was no ordinary Pokemon ability, he had been using. " _ **Now, my allies, RISE!**_ " The slime vibrated as if in response and began to collect into separate, large spheres. Gradually, shapes could be seen within the spheres of slime.

"Are those… Pokemon?" asked Lewis, peering into the inky darkness and withdrawing quickly. Each sphere exploded violently, showering the room in the slime, at the same time, revealing the creatures within. Five, darker, more sinister-like Pokemon stood in a circle around Arkah. In that group was a Machamp, a Nidoqueen, a Bisharp, a Reuniclus, and a Greninja, all the same shade as Arkah.

" _ **Now, my allies, let us go now, for time grows short...**_ " said Arkah, floating over to the door.

" _This isn't possible…_ " said Mercurius, his eyes wide and terrified. " _I-I… Arkah… how did you bring_ them _back…?_ "

" _ **...**_ " Arkah was silent. " _ **It would be best if you did not know that, Mercurius…**_ " With that, Arkah wrenched the door out of the doorway and added it to his armor. The five dark Pokemon followed him out into the hallway.

"Mercurius, what's wrong?" asked Lewis, looking over at him. "Who were those other Pokemon?"

" _Th-They..._ " Mercurius swallowed hard, and looked Lewis in the eye. " _They were the old experimental Pokemon… They… they were my friends before the humans killed them…_ "

"I-I don't know anything! I swear! Please don't- AGH!" The scream was accompanied by the sounds of bones being crushed in a very small amount of time.

" _Come Lewis, we mustn't let Arkah murder everyone here in cold blood,_ " said Mercurius, propping Layla up against the wall. " _Clark, you must stay here and watch over Layla, understand?_ " The turtle Pokemon nodded twice and sat beside Layla.

" _Now, we must go._ " Mercurius sprinted out the room with Lewis following as best as he could. The floor was drenched in deep red blood, giving off a horrible smell as it mixed with the black slime that the dark Pokemon seemed to ooze out.

"P-Please! D-Don't hurt me!" came a terrified scream from around a corner. Mercurius and Lewis dashed into the hallway just in time to see a scientist have his skull crushed in the fist of the Machamp.

" _Arkah, stop this madness!_ " yelled Mercurius. " _There are other ways than-_ "

" _ **Murdering? Is that what you were going to say, Mercurius?**_ " asked Arkah, growling. " _ **And yet, you know that there is no other way, don't lie to me, I can see right through you, Mercurius…**_ "

" _That may be so, but the humans are still living beings,_ " said Mercurius. " _You may be able to see right through me, but I know you intend to wipe out all of humanity, and not all humans are the same as-_ "

" _ **Are you honestly going to use**_ **that** _**card, against me? We both know that the entire world is like this, that no Pokemon is safe from the humans.**_ "

" _It is still not our responsibility to interfere with the way things Arceus intended-_ "

" _ **Arceus…? If he was so concerned with us, this would've never happened! So don't go around telling me that 'Arceus' had something planned, because he DOESN'T.**_ " Mercurius clenched his fists tightly, a slight blue aura forming around them. Arkah smiled wickedly, a purple aura forming around his own fists.

"Please, Arkah, can't we just work something out?" asked Lewis, suddenly getting in-between the two Pokemon.

" _What are you doing, Lewis?_ " asked Mercurius. " _This is not any other situation, you can die!_ "

"That doesn't matter! I know there's still some good left in Arkah… right?" Lewis looked at Arkah. "Right?"

" _ **Child… I spared you once, I won't do it twice…**_ " warned Arkah. Mercurius pushed Lewis aside.

" _This is none of your concern, Lewis,_ " said Mercurius, walking up.

"GET DOWN LEWIS!" Mercurius whirled around and tackled Lewis to the ground in one smooth motion. A large green projectile flashed by right before Lewis' eyes as he fell down. The projectile flew straight and plowed into the black mass that was the Machamp. The instant the two came into contact, the Machamp burst into a splatter of black droplets.

"Dad?!" exclaimed Lewis, looking up into the face of his father. Lewis' father now had a large gun in his hand connected by a tube to a large tank on his back. The whole weapon had biohazard and radiation symbols all over it. A green smoke floated out of the barrel of the gun.

"Get over here, Lewis, now," ordered Lewis' father. Mercurius leapt to his feet and looked at Lewis' father critically before turning back to face Arkah, now angrier than before.

" _ **Kill him!**_ " commanded Arkah, pointing at the cause of the Machamp's death. The four remaining dark Pokemon surged forward with bloodlust. Mercurius growled menacingly and leapt into combat, his arms glowing a deadly shade of blue.

"Dad! Aim for the black ones, but don't shoot Arkah!" said Lewis, pointing at the dark Pokemon. "And watch out for Mercurius.

"Lewis… I know what I'm doing," said Lewis' father through gritted teeth, taking aim at another dark Pokemon. "But this dang thing has too long of a cool down…"

" _ **RAAARGH**_!" The Nidoqueen suddenly appeared in directly in front of Lewis, roaring directly at him.

"Lewis!" The Nidoqueen swung its massive, armored claw downwards onto Lewis' head. He tried to move, but his feet refused to respond. Lewis felt a strange force envelope him, even as the claw came crashing down, and was forcefully dragged to the side. The claw smashed into the floor, creating huge gashes.

" _Lewis!_ " Clark came running into the hallway and up to Lewis. " _Dude, you okay?_ "

"Not yet!" yelled Lewis as the Nidoqueen swung her claw down again. This time, the Nidoqueen's arm didn't even go halfway before a bright green burst of energy blew apart the black slime that composed the Pokemon.

"Lewis, get back…" said Lewis' father, breathing heavily.

" _Come on man,_ " said Clark, leading Lewis to the back of the hallway where Layla stood against the wall, also breathing heavily. " _Layla's the one who did the whole jerking thing in case you didn't know._ "

"Wait! We can't just leave Mercurius!" Lewis gasped as he saw how the Lucario was faring against the Greninja, Bisharp, and Reuniclus. "He'll die if we don't do something!"

" _But what can we do…?_ " asked Layla in a tired voice.

" _ **NO! Kill the human!**_ " yelled Arkah, confusing Lewis as to why he himself wasn't going into combat. The dark Pokemon disengaged from Mercurius and sped over to Lewis' father.

"Dad!" Lewis broke into a sprint towards his father and tackled the Greninja.

"Lewis! What are you doing!?" demanded Lewis' father, narrowly avoiding a slice from the dark Bisharp. Mercurius intercepted the Bisharp and began to battle it. Lewis was violently pushed off of the Greninja and thrown backwards.

" _Lewis! Did we both not tell you to stay back!?_ " yelled Mercurius as he kicked the Bisharp back into the Reuniclus and the Greninja resumed its attack on Mercurius.

"Die all of you!" shouted Lewis' father, firing the superweapon directly into the Bisharp, sending black slime everywhere. Arkah grunted and looked at Lewis' father intent on murdering him.

" _ **Just. Kill. THE HUMAN!**_ " Arkah nearly screamed out. The two remaining dark Pokemon fought Mercurius off long enough to attack Lewis' father once more.

" _Stay away from him!_ " Mercurius, as tired and battered as he was, leapt back into action and wrestled the Greninja to the ground. " _Lewis! Grab the Reuniclus and keep it restrained!_ " Lewis took a deep breath and jumped at the Reuniclus, his arms outstretched. His fingers brushed by the sticky liquid of Reuniclus and he fell to the ground.

" _ **Prepare to die, human,**_ " said Arkah as Lewis' father was lifted into the air through Reuniclus' psychic power.

"Sucker…" Lewis' father smirked and unloaded another round of green energy into the Reuniclus. Arkah cried out in pain and glared at him.

" _ **KILL HIM-**_ "

"Kamehameha!" shouted Mercurius, cutting Arkah off as a bright blue beam of light seared through the dark Greninja's body, reducing it to ash.

"Why didn't you do that earlier?!" asked Lewis' father, a confused and angry look on his face, completely unsure whether or not Mercurius actually understood.

" _ **That's it. I am done with you filthy mortals… PREPARE FOR YOUR DOOM!**_ " Arkah's armor melted off and reforged themselves into needle-thin shards of metal floating just above his head.

"I wouldn't do that if I were you," warned Lewis' father, aiming his gun at Arkah, attempting to bluff his way through since the cooldown for the weapon was much longer, especially since he had used the shots in succession.

" _ **You wouldn't shoot me… no mortal could,**_ " said Arkah, scoffing.

"Oh really? Ya wanna try me?" Lewis' father leveled the barrel of the gun with Arkah's head. "Go ahead, try me."

"Dad… I know that I said to not hurt Arkah… but…" Lewis bit his lower lip in deep contemplation. "I'm not so sure anymore…"

" _I too, would've preferred if we could end this without bloodshed, but it would appear that Arkah will not give up without a fight,_ " agreed Mercurius. Lewis' father tightened his finger around the trigger of the gun, smiling now that the cooldown had finished.

" _ **If you continue on this path, human, I guarantee it will not end happily,**_ " said Arkah, making the metal shards spin.

"Oh just die already." Lewis' father fired the gun at the same time Arkah telekinetically launched the metal shards at him. Time seemed to slow down. The green energy flowed smoothly towards Arkah, but just before it hit him, something peculiar happened. Lewis could see Arkah smirk and suddenly, Lewis was looking straight into the bright light of the incoming energy attack.

"NOO!" yelled Lewis' father, his eyes widening as the metal shards made contact with him and the green energy made contact… with Lewis. It was an ability that Mercurius had spoken of once. Ally Switch, it was called, and it allowed the user to switch with its ally during combat. One moment, Lewis was wondering how he had gotten in front of the green energy, the next, he felt an incredible piercing pain in his abdomen and he was flying backwards into a wall. Then, everything went black.

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 **The end of the 2nd chapter. Cool. So, what did you think of this chapter? Was it good? Was it bad? Was it just "meh"? Just tell me in the reviews if you have the time and patience to write something like that. Well, that's it for now, see you whenever I post another chapter, ciao!**


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